Interpretive Summary: Creeping wildrye(Leymus triticoides) and basin wildrye (Leymus cinereus) are divergent perennial grasses, which form fertile hybrids. Genetic maps of the 14 chromosomes have been used for mapping quantiative trait loci (QTLs) in these hybrids, and chromosomes of other Leymus wildryes have been transferred to wheat. However, identifications of the chromosomes were uncertain and genetic research in these grasses has been encumbered by a lack of functional gene marker sequences. Herein, we mapped 376 Leymus wildrye gene sequences including 26 putative lignin biosynthesis genes and constructed one new integrated consensus map. Chromosomes maps LH1b and LG6b were reassigned as LG6b* and LGlb*, respectively, and LG4Ns and Lg4Xm were inverted so that all 14 chromosome maps are aligned to the chromosome maps of wheat, barley, and other cereal grasses. Amplification of 146 mapped Leymus genes representing six of the seven basic chromosomes groups was shown for 17 wheat-Leymus chromosome introgression lines. Translocation of DNA between Leymus chromosomes 4 and 5 show are similar to a translocation between chromosomes 4 and 5 of the wheat ancestor Triticum monococcum, which may be a related characteristic of these species. The caffeic acid O-methyltransferase lignin biosynthesis gene aligned to forage quality QTL peaks on Leymus chromosomes LG7a and brown midrib mutations of forage-type maize and sorghum. Likewise, genes controlling leaf wax synthesis in Leymus and wheat map to the same region of chromosome 2. Markers linked to the S self-incompatibility mating gene on Leymus chromosome LG1a interact with genes on LG2b. Homoeologous chromosomes 1 and 2 harbor the S and Z gametophytic self-incompatibility mating genes of other grasses including reed canary grass cereal rye, and perennial ryegrass but the Leymus chromosome-2 self-incomatibility gene maps to a different locus. Nevertheless, the interaction of self-incompatibility genes on Leymus chromosomes 1 and 2 presents a powerful system for genetic mapping both genes.

Technical Abstract:
Allotetraploid (2n-4x-28) Leymus triticoides and Leymus cinereus are divergent perennial grasses, which form fertile hybrids. Genetic maps with n=14 linkage groups (LG) comprised of 1,583 AFLP and 67 heterologous anchor markers have been used for mapping quantitative trait loci (QTLs) in these hybrids, and chromosomes of other Leymus wildryes have been transferred to wheat. However, identifications of the x=7 homoeologous groups were tenuous and genetic research has been encumbered by a lack of functional, conserved gene marker sequences. Herein, we mapped 350 SSR and 26 putative lignin biosynthesis genes from a new Leymus EST library and constucted one integrated consensus map with 799 markers, including 375 AFLPs and 48 heterologous markers, spanning 2,381 centiMorgans. LG1b and LG6b were reassigned as LG6b* and LGlb*, respectively, and LG4Ns and LG4Xm were inverted so that all 14 linkage groups are aligned to the x=7 Triticeae chromosomes based on EST alignments to Hordeum and other reference genomes. Amplification of 146 mapped Leymus ESTs representing six of the seven homoeologous groups was shown for 17 wheat-Leymus chromosome introgression lines. Reciprocal translocations between 4L and 5L in both Leymus and Triticum monococcum were aligned to the same regions of Brachypodium chromosome 1. A caffeic acid O-methyltransferase locus aligned to fiber QTL peaks on Leymus LG7a and brown midrib mutations of maize and sorghum. Glaucousness genes on Leymus and wheat chromosome 2 were aligned to the same region of Brachypodium chromosome 5. Markers linked to the S self-incompatibility gene on Leymus LG1a cosegregated with markers on LG2b, possibly cross-linked by gametophytic selection. Homoeologous chromosomes 1 and 2 harbor the S and Z gametophytic self-incompatibility genes of Phalaris, Secale, and Lolium, but the Leymus chromosome-2 self-incompatibility gene aligns to a different region on Brachypodium chromosome 5. Nevertheless, cosegregation of self-incompatibility genes on Leymus presents a powerful system for mapping.